RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.lDU1Iy/RM_1793821.FriSep122057572025 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1757735877 Database = /dev/shm/rModeler.lDU1Iy/GCA_051529475.1_YNP35 - Sequences = 9516 - Bases = 25223953 - N50 = 3373 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 49626-53157 | [ 1 ] 46096-49626 | [ ] 42565-46095 | [ ] 39035-42565 | [ ] 35505-39035 | [ ] 31974-35504 | [ ] 28444-31974 | [ 1 ] 24913-28443 | [ 2 ] 21383-24913 | [ 2 ] 17853-21383 | [ 14 ] 14322-17852 | [ 27 ] 10792-14322 | [ 93 ] 7261-10791 |** [ 340 ] 3731-7261 |******** [ 1326 ] 201-3731 |************************************************** [ 7710 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = excellent ( 1703.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 25223853 bp ( 24955417 non ambiguous ) - Num Contigs Represented = 9516 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 139 raw families identified - RepeatScout: Running filtering stage.. 137 families remaining - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 131 families... 00:00:17 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 35 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:57 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2312 repeats masked totaling 563706 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10107011 bp Num Contigs Represented = 3868 Non ambiguous bp: Initial: 10001420 bp After Masking: 9398241 bp Masked: 6.03 % -- Input Database Coverage: 10107011 bp out of 25223953 bp ( 40.07 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7478778 Comparison Time: 00:16:07 (hh:mm:ss) Elapsed Time, 16347 HSPs Collected Number of families returned by RECON: 2485 Round Time: 00:16:32 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4633 repeats masked totaling 969219 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 15116774 bp Num Contigs Represented = 5648 Non ambiguous bp: Initial: 14953929 bp After Masking: 13925840 bp Masked: 6.88 % -- Input Database Coverage: 25223785 bp out of 25223953 bp ( 100.00 % ) Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 15952776 Comparison Time: 00:24:00 (hh:mm:ss) Elapsed Time, 20172 HSPs Collected Number of families returned by RECON: 3558 Round Time: 00:24:36 (hh:mm:ss) Elapsed Time : 41 families discovered. RepeatScout/RECON discovery complete: 155 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.lDU1Iy/RM_1793821.FriSep122057572025 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:00:14 (hh:mm:ss) Elapsed Time Program Time: 00:42:19 (hh:mm:ss) Elapsed Time